GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer2_BFD - BFD-like 2Fe-2S binding domain
Pfam: PF04324 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Length: 55
Sequences: 2825
Seq/Len: 51.36
HH_delta: -0.034 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
26_T29_E1.037232.142
11_E15_R0.869211.795
10_T13_E0.837171.729
22_N33_A0.836491.728
25_R29_E0.83541.726
2_I10_T0.808211.669
48_K52_A0.78461.621
14_I30_I0.758031.566
7_N35_G0.743381.535
7_N39_G0.741861.532
44_V48_K0.728441.505
36_A47_V0.721631.491
24_A30_I0.712661.472
3_V14_I0.710811.468
18_I51_L0.678831.402
27_L31_K0.673851.392
31_K38_T0.665431.374
47_V51_L0.637421.317
17_A34_T0.633571.309
2_I8_G0.604731.249
28_E32_R0.581391.201
15_R53_E0.574631.187
29_E33_A0.557311.151
27_L44_V0.550381.137
13_E16_D0.549561.135
30_I51_L0.544561.125
37_G44_V0.539341.114
16_D22_N0.534491.104
12_G16_D0.508541.050
27_L47_V0.492111.016
46_E49_D0.48831.009
5_R35_G0.486741.005
15_R19_R0.47760.986
15_R50_L0.473920.979
31_K37_G0.451280.932
30_I36_A0.447990.925
5_R42_S0.446020.921
24_A33_A0.435590.900
2_I5_R0.433480.895
40_C43_C0.43050.889
42_S46_E0.419780.867
27_L48_K0.408990.845
7_N38_T0.389710.805
27_L51_L0.378980.783
35_G38_T0.366650.757
4_C43_C0.365980.756
9_V34_T0.365480.755
7_N31_K0.361670.747
42_S45_P0.359690.743
17_A30_I0.357970.739
18_I23_G0.357220.738
29_E32_R0.351030.725
11_E53_E0.347930.719
3_V11_E0.339330.701
19_R22_N0.338750.700
45_P48_K0.333340.689
9_V31_K0.318510.658
30_I47_V0.314770.650
24_A29_E0.310780.642
18_I47_V0.309310.639
2_I28_E0.305840.632
9_V36_A0.302090.624
5_R41_G0.296250.612
14_I34_T0.295480.610
17_A24_A0.293850.607
4_C40_C0.29290.605
6_C43_C0.285250.589
19_R25_R0.281050.581
9_V38_T0.279480.577
37_G50_L0.266770.551
11_E46_E0.265560.549
6_C36_A0.259870.537
24_A51_L0.259580.536
18_I50_L0.255450.528
32_R38_T0.252330.521
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
4e6kG0.963699.3-0.034
2gagA0.963698.90.168
1y56A0.945598.40.302
2hu9A0.909198.30.331
2qcuA194.10.628
2rghA0.981852.60.759
1vq0A0.927319.50.806
3i4pA0.836419.30.807
1vzyA0.927316.90.812
2k02A0.945515.40.815

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